Thursday, 18 December 2014

I used the title of this post as a heading when discussing
the extraordinary adaptations shown by some organisms [1]. The examples I chose
to illustrate this point were female bolas spiders and the larvae of black
flies. Female bolas spiders use a sticky blob of silk on the end of a line that
they use to drop on moths attracted to the smell that they produce, mimicking a
pheromone produced by female moths. Silk is also used by blackly larvae, both
for attachment and for building a cocoon in which pupation occurs. However,
their remarkable feature is their head fans that are wonderful examples of
precision engineering and which fold to allow the larva to remove tiny
particles that have been trapped from currents of water.

These were just two examples from a huge number in Natural
History where one’s sense of wonder forces the question “How did that evolve?”.
Recently, a further example of extraordinary adaptations was reported. The
Cinereous Mourner (Laniocera hypopyrra)
is a grey bird that is relatively common in the northern Amazon rain forest (see below centre). The chick is quite different in appearance and has orange-red, spiky plumage,
with white tips to each spike, that causes it to resemblepoisonous caterpillars of similar size (of
the genera Megalopyge or Podalia [2] - a Podalia larva is shown below left; a Laniocera chick, below right).

Not only does the bird look like a
caterpillar; it also moves like one:

In their paper, to be published in The American Naturalist in January 2015 [2], Gustavo A. Londoño, Duván A. García and
Manuel A. Sánchez Martínez suggest that, as the young
chicks of this species are highly vulnerable to predation, mimicry of a
poisonous caterpillar reduces the risk of attack. Chicks are slow-growing and
do not beg for food like other nestlings, so their behavioural responses, as
well as their appearance, are under genetic control. After about 16 days, the
behaviour of the chicks changes, as they become more mobile and can avoid
attackers. At this time the downy feathers begin to drop and the adult, grey
plumage begins to emerge. The authors write:

The close match in size,
morphology, and behavior between the nestling and the caterpillar supports the
hypothesis of Batesian mimicry being used by the nestling, possibly to reduce
nest predation. Therefore, nestling morphological and behavioral characteristics
could have evolved as a result of the combination between the slow life-history
nesting strategy observed in L. hypopyrra
(e.g., long nestling period) and the high nest-predation pressures observed at
the study site.

I agree, but how did this evolve and over what time period?
Were there chance mutations that caused the changes of appearance and behaviour
that coincidentally mimicked poisonous caterpillars of similar size? It must be
so, although it is very difficult to see what the steps in the process might
have been. Were there dramatic mutations, or a sequence of much smaller ones? If
the latter, how were they selected if they conveyed only a tiny advantage at
each step, or no advantage at all? There are so many questions, but no answers -
only much speculation. Do you see what I mean when I say that believing in
Creation can seem like an easy option?

Friday, 12 December 2014

The celebration of Christ’s birth has been superimposed on
a winter solstice festival and many of the familiar features we know today were
added in the 19th Century. As a result of this pagan origin, some Christians refuse
to celebrate Christmas, with all its familiar foods and decorations. Historically,
Philip Henry Gosse, the distinguished Victorian Natural Historian and member
of the Brethren, was probably the most famous of these objectors. In Father and Son, Edmund Gosse describes
how his father reacted when discovering a plum pudding in the house in St Marychurch [1]:

On Christmas Day.. ..1857 our
villa saw a very unusual sight. My Father had given strictest charge that no
difference whatever was to be made in our meals on that day; the dinner was to
be neither more copious than usual nor less so. He was obeyed, but the
servants, secretly rebellious, made a small plum-pudding for themselves..
..Early in the afternoon, the maids.. ..kindly remarked that ‘the poor dear
child ought to have a bit, anyhow’, and wheedled me into the kitchen, where I
ate a piece of plum-pudding. Shortly I began to feel that pain inside which in
my frail state was inevitable, and my conscience smote me violently. At length
I could bear my spiritual anguish no longer, and bursting into the study I
called out: ‘Oh! Papa, Papa, I have eaten of flesh offered to idols!’ It took
some time, between my sobs, to explain what had happened. Then my Father
sternly said: ‘Where is the accursed thing?’ I explained that as much as was
left of it was still on the kitchen table. He took me by the hand, and ran with
me into the midst of the startled servants, seized what remained of the
pudding, and with the plate in one hand and me still tight in the other, ran
till we reached the dust-heap, when he flung the idolatrous confectionery on to
the middle of the ashes, and then raked it deep down into the mass..

A rather extreme reaction, although Ann Thwaite, the biographer of both Henry and Edmund Gosse, warns us that Edmund
was prone to inaccuracy and that the story may be exaggerated. However, Dr
Thwaite writes that she “really want(s) to believe the story of the plum
pudding being flung onto the dust heap” [2] and it is a splendid piece of
storytelling by Edmund. Henry Gosse, a warm and wonderful man in many ways, is
caste in a very stern light and he was certainly inflexible on matters of
religious belief. He would never compromise and this eventually led to the
breakdown of his relationship with Edmund, something that pained them both.

Like Edmund Gosse, I was brought up in a Christian household,
but one that was much less restrictive when it came to Christmas. The build-up
began at school, where a Nativity Play was performed by one class during a
special assembly (there are no pictures of our play, but a similar event is
shown below). Choosing the children for each of the roles must have been taxing
for the teachers and there was probably hot competition (in the eyes of some parents,
anyway) for the star roles. I was not aware of this, but, when it was our turn
in the late 1950s, was chosen to be a King, one of the bigger parts. I wore a
blue and red tablecloth, sewn in a complicated way to make armholes, and a
turban made from the cut-off crown of one of my mother’s felt hats, to which bright
cloth had been stitched. My gift of gold took the form of a brass flower vase,
kindly donated by Great Aunt Nell for the occasion.

A few days later came the school carol service, held in Paignton Parish Church, and then, on the last Sunday before Christmas Day, we
attended one in Winner Street Baptist Church where our family worshipped. These services
were very enjoyable as the tunes of carols are marvellous and fun could
be had by altering some of the words....“While shepherds washed their socks by
night....”; etc. I think I’m correct in remembering that there was also a model
nativity scene in both churches, with the same characters that we had in the
school Nativity Play, although with a few less angels, as so many bit-part actors
had to be accommodated in the latter. Henry Gosse would have protested at such
idolatry.

When growing up, I had no idea that all the fun of Christmas
Day had pagan origins, thinking that everything was part of the celebration of
the birth of Christ: how gifts from
Kings (Wise Men, Magi) to Jesus became modified into presents from Father Christmas
(Santa Claus, Kris Kringle, parents) to me was a mystery. It was the only time in the year when we spent the whole day
in the front room and it was decorated with paper streamers of various types, hung from corner
to corner and along the walls. Excitement built through Christmas Eve and, very
early on the morning of Christmas Day, the most nerve-tingling part was finding
one of my mother’s old lisle stockings at the foot of my bed, packed with sweets,
toys and with an orange in the toe. At some early hour, the stocking was
dragged into my parents' room and Christmas could begin. There was an exchange
of presents and we moved downstairs once the coal fires had been lit and the
lower part of the house became bearably warm.

There were new toys to play with
and books to read before we had lunch and this was always centred on a large
chicken, the only time we ate a bird during the year. In addition, there were roast potatoes,
Brussels sprouts, bread sauce, stuffing, and gravy but, of course, no alcoholic drinks This feast was followed
by the plum pudding that was brought to the table fresh from the steamer. It
was a family tradition that the plum pudding was always made by Great Aunt Ede sometime
in October and we went to collect it just before Christmas. It was made in a
china basin, with greaseproof paper and muslin tied tightly around the rim, the
ends of the muslin being knotted over the top to form a handle. We never discovered
the recipe, but knew that silver threepenny pieces had been buried in it at
some point and that finding one of these in a slice of pudding brought luck (clearly,
superstitions were allowed in our Christian household). The rest of the day was
an anti-climax and we just munched on nuts and chocolate, listened to the
Queen’s speech on the radio, and then went back to playing, reading and dozing.

I’m grateful for the happy memories and it was all very different from the way December 25th was spent in the Gosse household a hundred years before. We must have been rather different Christians.

Friday, 5 December 2014

I have always enjoyed walking along river banks. While
torrential rivers are awesome, especially when they are flooded after snow
melt or very heavy rains, there is a special quality of calmness that comes
from strolling through the meadows that border tranquil chalk streams. I am
fortunate in living near one of the most attractive of these streams, the River
Chess, which is fed by water from springs connected to reservoirs of clear
water in the underlying chalk strata.

Picture
from River Chess Association Facebook Page [1]

Chalk streams are rare worldwide, although there are a fair
few of them in England, and they are of such importance that a report, The State of England’s Chalk Streams,has been prepared by WWF-UK [2].On page 39 of the report, I found this:

“RIVER CHESS

In 2014, high groundwater levels
overwhelmed Thames Water’s Chesham Sewage Treatment Works, and for four months
(February to June 2014) raw sewage mixed with groundwater continuously entered
the river. The impact of this pollution is not fully known but the River Chess
Association volunteers have observed dead fish, significant amounts of sewage
fungus and fewer riverfly downstream of the sewage outfall pipe. They have also
had to cancel school trips and planned river restoration works due to risks to
human health. While the water company has few choices in the circumstances in order
to prevent sewage flooding homes, the problem is a result of years of
underinvestment. Even in normal conditions, the plant is working close to
capacity and the slightest stress can cause failures.”

I am sure that Thames Water did not intend to release untreated sewage into the River Chess, but they must prefer this to the
consequences of passing it on to land or into property (although treated sewage
is applied to land as a fertiliser [3]). There are two good reasons for this.
Firstly, the pollution is not as visible as it would be on land and, secondly,
flowing water carries the discharges away from the site of input and this conveniently
spreads the impact.

The microbial community of all natural water bodies has evolved
to convert solid and dissolved organic matter into nutrients that support both
the growth of microbes and also that of plants. Inputs may be in the form of
leaves that fall into the river; in situ
vegetation after die-back; animal bodies; natural waste products in both solid
and dissolved form; etc. Adding sewage provides a burden, but the natural community
utilises this input and the effects are moderated as a result. Of course, if
the effluent contains heavy metals or other conservative pollutants, there are
more serious problems and an excess of nutrients can cause changes in oxygen
tension, although this is mediated by the water being aerated as it flows
downstream. The shallow nature of chalk streams helps in this regard, but it
also means that settlement to, and within, the substratum and trapping on in-stream
vegetation is also enhanced. There can also be local choking with “sewage
fungus” (below), as seen on the River Chess, this being a complex community of filamentous
bacteria with fungi and other bacteria, all bound with sticky exudates produced
by these organisms. “Sewage fungus” is colonised by populations of protozoans
and invertebrates and remains for some time after the input of pollution, with
a corresponding clogging and shading effect on the rest of the community of
organisms in the stream or river. However, the water bodies do recover.

It is interesting that the transformation of organic
matter by microbes in running waters is replicated in the methods used by
the water industry to clean effluent, with some sewage treatment plants using
trickling filters and others activated sludge tanks. Before these treatments, effluent
from the sewerage system is screened and then passed into settlement tanks to
allow larger particles to fall out and form sediment. Organically-rich water is
then treated by one of the two methods. It may either be passed through
rotating radial pipes to the surface of a trickling filter formed of a thick
bed of porous material (below left), or it will be passed into tanks that are aerated,
or stirred, vigorously (below right) and then seeded with microbial floc from a
previous activated sludge treatment. In the trickling filter, the cleaning
agents are bacteria and fungi that grow in biofilms over the surface of the substratum
and also though the pores it contains, just as they do over, and within, the substratum
of streams and rivers. The microbial community in the beds grows vigorously and
the whole system risks becoming clogged, but this is averted by abundant
single-celled organisms and invertebrates that graze over the accumulated biofilm
and therefore stimulate the production of new, freshly adsorptive surfaces. In contrast,
the growth of bacteria (it is mainly bacteria) in the aerated/stirred activated
sludge tanks results in the formation of flocs and other aggregates in the
water column that are bound by the exudates of bacteria and these sediment to
allow removal. It is these flocs, together with the bacteria themselves, which
remove organic matter in both fine particulate and dissolved form. This is a
process that occurs naturally in streams and rivers (although at a much less
intense scale), especially where there is turbulence or the inclusion of large
numbers of bubbles [4] It is the biological community that does the work of
cleaning the incoming effluent and water engineers design the most effective
plant to optimise biological activity - until something goes wrong.

So, where does the effluent come from? Understandably, we
show a lot of interest in what we eat and drink, the various methods of food preparation,
and the delights of flavours and textures. However, we all know that the material
entering our digestive system becomes transformed and passes from our bodies on
a regular basis. Although solid wastes were once the subject of attention [5],
the topic of excretion is now forbidden in polite company, except among the parents of infants.
Fortunately, houses and work places in advanced civilisations have water
closets that mean we do not have to face the unmentionable for more than a few
minutes each day.

Being terrestrial animals, humans have always considered
water as an ideal dumping ground, as material thrown into the sea, into lakes, or
into rivers quickly disappears from sight and smell. The first settlers by the
River Chess disposed of waste products downstream, while taking clean water
from the river upstream from their settlements. That continues to happen today,
but on a much larger scale, with clean water for drinking (and for all the other
uses of drinking water - watering gardens, cleaning cars, etc.) being taken from the reservoirs in the
chalk, while wastes (from water closets, but also sinks and drains in the town of
Chesham) are passed through the sewage works before cleaner water goes back
to the river. That is what is meant to happen, but recent events, based on a
lack of foresight and investment, has sent us back to more primitive times.

The river will recover, but why do we take
this for granted and why do we compromise the future of something so pleasing
aesthetically? The simple answer is that we don’t care, or don’t care enough,
and I include myself in that apathy. Human interests will always exceed those
of the environment, even if that environment is one as beautiful and precious as
the River Chess. Come on Thames Water, take the lead and make the investment in
Nature. After all, you depend on living communities to treat effluent and they
work for you for free.

Thursday, 27 November 2014

I recently took a course in cosmology in the hope of trying
to fill some voids in my knowledge. We were spared all the mathematics that are
needed for a comprehensive understanding, but the excellent tutor certainly put
across key points on the age of the universe, its size, its changes through time,
and the features of some of its components. My knowledge remains
superficial, but it is enough for me to realise that it is impossible to get
any real sense of the distances and times involved and humans will never be
able to do this as the numbers are so large that we cannot compare them with with
anything familiar to us. Another impression that the cosmology course left with
me was that some explanations of events and structures are close to being
science fiction.

The topic that created most enthusiasm among
members of the class was discussion of the origin of life and whether living
organisms exist elsewhere. The desire to find organisms has extended to looking
for chemicals that may be involved in their make-up and we also make projections
about possible habitats; a popular one being to equate finding water on other
planets, or in other parts of the Universe, as being tantamount to finding
living organisms. We are interested especially in the possibility of
intelligent life, with which we can communicate, providing us with a feeling
that we are not alone.

It was clear that most of us in the cosmology class had
varying views on what we meant by life, with most thinking that it was only
possible in a distinct organism, perhaps consisting of one cell, perhaps of
several cells. So, is there an agreed definition? As a starting
point, I read Schrödinger’s What is Life?, based on a series of
lectures he gave at Trinity College Dublin in 1943 [1]. Schrödinger’s discourse detailed the way
in which cells, and thus multicellular organisms, were controlled by the
physics and chemistry of genes (although the mechanism of control was not known
until the structure of DNA was discovered 10 years later). I would like to
quote two sections [1]:

What is the characteristic
feature of life? When is a piece of matter said to be alive? When it goes on
‘doing something’, moving, exchanging material with its environment, and so
forth, and that for a much longer period than we would expect of an inanimate
piece of matter to ‘keep going’ under similar circumstances.

The unfolding of events in the
life cycle of an organism exhibits an admirable regularity and orderliness,
unrivalled by anything we meet in inanimate matter. We find it controlled by a
supremely well-ordered group of atoms, which represent only a very small
fraction of the sum total in every cell. Moreover, from the view we have formed
of the mechanism of mutation we conclude that the dislocation of just a few atoms
from within the group of ‘governing atoms’ of the germ cell suffices to bring
about a well-defined change in the large-scale hereditary characteristics of
the organism.

I am comfortable with Schrödinger’s view that life is a feature of organisms and that the
biology of organisms is under the control of what we now know to be DNA.
However, we still lack a definition of life and, for this, I turned to Pincock and Frary's The Origins of the Universe for Dummies.
Having reviewed complexity, metabolism, development, autonomy and reproduction,
the authors write [2]:

Taking all the elements we
describe in the previous sections, and all their shortcomings, into account, we
can come up with a simple, one-sentence definition of life. (Of course, scientists
tell you that this description isn’t perfect, but it serves as a rough
definition, at least for now.)

Here’s the working definition,
which is sometimes known as the NASA
definition of life: Life is a
self-sustaining chemical system capable of Darwinian evolution [my
emboldening].

There is no mention of organisms here and it is a definition
that is difficult for all to accept, as Pincock and Frary anticipated.

It has been pointed out that there is unlikely ever to be
agreement on a definition of life. Carol Cleland and Christopher Chyba write
[3]:

The philosophical question of the
definition of ‘life’ has increasing practical importance. As science makes
progress towards understanding the origin of life on Earth, as laboratory
experiments approach the synthesis of life (as measured by the criteria of some
definitions), and as greater attention is focused on astrobiology and the
search for life on Mars and Jupiter’s moon Europa, the utility of a general
definition grows. In particular, definitions of ‘life’ are explicit or implicit
in any remote in situ search for extraterrestrial life.

Is science making progress towards understanding the origin
of life on Earth and do laboratory experiments approach the synthesis of life? I
question whether this is so, but, as Cleland and Chyba point out, it depends on
the definition used. Does anyone consider DNA to be alive? Isn’t there an elusive essence
to life that involves more than the interaction of molecules? Isn’t that what Schrödinger implied?

Cleland and Chyba’s Abstract is worth quoting [3]:

There is no broadly accepted
definition of ‘life’ Suggested definitions face problems, often in the form of
robust counter-examples. Here we use insights from philosophical investigations
into language to argue that defining ‘life’ currently poses a dilemma analogous
to that faced by those hoping to define ‘water’ before the existence of molecular
theory. In the absence of an analogous theory of the nature of living systems,
interminable controversy over the definition of life is inescapable.

How true. One reason that I left a University astrobiology research group was because we all talked
about life, but there was no consensus on what we meant. I couldn’t sit back
and listen to colleagues talking about the origin of life when they really
meant the first appearance of RNA and DNA. I had similar problems when listening
to them, and others, saying that life probably originated in hydrothermal vents;
that extremophile microorganisms are likely to be found in extraterrestrial habitats with similar
harsh conditions to those where these extraordinary organisms live on Earth; etc. While it would be wonderful to find living cells, or conclusive
evidence of living cells having been present, on moons or planets elsewhere in
the solar system (or elsewhere in the Universe), I’m not expecting such discoveries
to be made, as I remain convinced that the first living cell formed on Earth in
a once and once only event. Isn't that the best working hypothesis until we can
prove otherwise?